TCM‐Suite: A comprehensive and holistic platform for Traditional Chinese Medicine component identification and network pharmacology analysis. Issue 4 (15th August 2022)

• Record Type: Journal Article
• Authors: Yang, Pengshuo; Lang, Jidong; Li, Hongjun; Lu, Jinxiang; Lin, Hanyang; Tian, Geng; Bai, Hong; Yang, Jialiang; Ning, Kang
• Is Part Of: IMeta. Volume 1:Issue 4(2022)
• Page Start: n/a
• Page End: n/a
• Publication Date: 2022-08-15
• Subjects: composition identification -- database -- holistic pipeline -- network pharmacology -- Traditional Chinese Medicine -- webserver; Metagenomics -- Periodicals; Bioinformatics -- Periodicals; Bioinformatics; Metagenomics; Metagenomics; Metagenome; Computational Biology; Periodicals; Periodical; 576.5
• DOI: 10.1002/imt2.47
• Languages: English
• ISSNs: 2770-596X

Abstract

Abstract: DNA‐based biological ingredient identification and downstream pharmacology network analysis are commonly used in research for Traditional Chinese Medicine preparations (TCM formulas). Advancements in bioinformatics tools and the accumulation of related data have become driving forces for progress in this field. However, a lack of a platform integrating biological ingredient identification and downstream pharmacology network analysis hinders the deep understanding of TCM. In this study, we developed the TCM‐Suite platform composed of two sub‐databases, Holmes‐Suite and Watson‐Suite, for TCM biological ingredient identification and network pharmacology investigation, respectively, both are among the most complete: In the Holmes‐Suite, we collected and processed six types of marker gene sequences, accounting for 1, 251, 548 marker gene sequences. In the Watson‐Suite, we curated and integrated a massive number of entries from more than 10 public databases. Importantly, we developed a comprehensive pipeline to integrate TCM biological ingredient identification and downstream network pharmacology research, allowing users to simultaneously identify components of a TCM formula and analyze its potential pharmacology mechanism. Furthermore, we designed search engines and a user‐friendly platform to better search and visualize these rich resources. TCM‐Suite is a comprehensive and holistic platform for TCM‐based drug discovery and repurposing. TCM‐Suite website: http://TCM-Suite.AImicrobiome.cn . Abstract : TCM‐Suite platform is composed of two sub‐databases, Holmes‐Suite and Watson‐Suite. Holmes‐Suite database covers six marker genes, resulting in 235, 470 kinds of biological ingredients. Watson‐Suite retrieved massive data for mining the "herb‐compound‐protein‐disease" interpretation. A holistic pipeline was designed to connect Holmes and Watson, showed by a user‐friendly platform. Highlights: TCM‐Suite platform is composed of two sub‐databases, Holmes‐Suite and Watson‐Suite. Holmes‐Suite database covers six marker genes, resulting in 235, 470 kinds of biological ingredients. Watson‐Suite retrieved massive data for mining the "herb‐compound‐protein‐disease" interpretation. A holistic pipeline was designed to connect Holmes and Watson, shown by a user‐friendly platform.